{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T20:44:39Z","timestamp":1761597879937,"version":"3.37.3"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2017,11,23]],"date-time":"2017-11-23T00:00:00Z","timestamp":1511395200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HL-095056, HL-28481"],"award-info":[{"award-number":["HL-095056, HL-28481"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["F31HL127921"],"award-info":[{"award-number":["F31HL127921"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["T32HG002536"],"award-info":[{"award-number":["T32HG002536"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Mapping bias causes preferential alignment to the reference allele, forming a major obstacle in allele-specific expression (ASE) analysis. The existing methods, such as simulation and SNP-aware alignment, are either inaccurate or relatively slow. To fast and accurately count allelic reads for ASE analysis, we developed a novel approach, ASElux, which utilizes the personal SNP information and counts allelic reads directly from unmapped RNA-sequence (RNA-seq) data. ASElux significantly reduces runtime by disregarding reads outside single nucleotide polymorphisms (SNPs) during the alignment.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>When compared to other tools on simulated and experimental data, ASElux achieves a higher accuracy on ASE estimation than non-SNP-aware aligners and requires a much shorter time than the benchmark SNP-aware aligner, GSNAP with just a slight loss in performance. ASElux can process 40 million read-pairs from an RNA-sequence (RNA-seq) sample and count allelic reads within 10\u2009min, which is comparable to directly counting the allelic reads from alignments based on other tools. Furthermore, processing an RNA-seq sample using ASElux in conjunction with a general aligner, such as STAR, is more accurate and still \u223c4\u00d7 faster than STAR\u2009+\u2009WASP, and \u223c33\u00d7 faster than the lead SNP-aware aligner, GSNAP, making ASElux ideal for ASE analysis of large-scale transcriptomic studies. We applied ASElux to 273 lung RNA-seq samples from GTEx and identified a splice-QTL rs11078928 in lung which explains the mechanism underlying an asthma GWAS SNP rs11078927. Thus, our analysis demonstrated ASE as a highly powerful complementary tool to cis-expression quantitative trait locus (eQTL) analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The software can be downloaded from https:\/\/github.com\/abl0719\/ASElux.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx762","type":"journal-article","created":{"date-parts":[[2017,11,22]],"date-time":"2017-11-22T20:13:53Z","timestamp":1511381633000},"page":"1313-1320","source":"Crossref","is-referenced-by-count":17,"title":["ASElux: an ultra-fast and accurate allelic reads counter"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6183-4565","authenticated-orcid":false,"given":"Zong","family":"Miao","sequence":"first","affiliation":[{"name":"Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA"},{"name":"Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA"}]},{"given":"Marcus","family":"Alvarez","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA"}]},{"given":"P\u00e4ivi","family":"Pajukanta","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA"},{"name":"Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA"},{"name":"Molecular Biology Institute, UCLA, Los Angeles, CA, USA"}]},{"given":"Arthur","family":"Ko","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA"},{"name":"Molecular Biology Institute, UCLA, Los Angeles, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,11,23]]},"reference":[{"key":"2023012713005790800_btx762-B1","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1126\/science.1262110","article-title":"The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans","volume":"348","author":"Ardlie","year":"2015","journal-title":"Science"},{"key":"2023012713005790800_btx762-B2","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/ng.2830","article-title":"A genome-wide association study identifies CDHR3 as a susceptibility locus for early childhood asthma with severe exacerbations","volume":"46","author":"B\u00f8nnelykke","year":"2014","journal-title":"Nat. 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